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PanDDA analysis group deposition Form1 MAP kinase p38-alpha -- Fragment N13470a in complex with MAP kinase p38-alpha
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6SO1 PDB entry 6SO1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.9 291 27.5% PEG3350, 0.1 M Bis-Tris propane, pH 6.9, 50 mM ammonium sulfate, 0.2 M 1:1 magnesium chloride:magnesium sulfate,
10% glycerol
Crystal Properties Matthews coefficient Solvent content 3.04 59.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.785 α = 90 b = 86.041 β = 90 c = 127.473 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2016-02-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92819 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.7 29.29 98.4 0.06 0.065 0.025 0.999 19.6 6.6 55358
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.74 95.1 0.823 0.891 0.339 0.709 6.7 3912
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT PDB entry 6SO1 1.7 29.3 52548 2757 97.99 0.1814 0.1805 0.2226 0.1986 0.2291 RANDOM 26.622
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -0.05 -0.01 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.714 r_dihedral_angle_4_deg 17.615 r_dihedral_angle_3_deg 16.765 r_dihedral_angle_1_deg 6.453 r_mcangle_it 3.459 r_mcbond_other 1.972 r_mcbond_it 1.957 r_angle_refined_deg 1.599 r_angle_other_deg 1.354 r_chiral_restr 0.076
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.714 r_dihedral_angle_4_deg 17.615 r_dihedral_angle_3_deg 16.765 r_dihedral_angle_1_deg 6.453 r_mcangle_it 3.459 r_mcbond_other 1.972 r_mcbond_it 1.957 r_angle_refined_deg 1.599 r_angle_other_deg 1.354 r_chiral_restr 0.076 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2746 Nucleic Acid Atoms Solvent Atoms 238 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing